I was having the same issue as you , tried a new relay on the fender also did a new connector on the orange wire still had intermittent problems not priming the fuel rail so I unplugged the connector at the tank for my hotwire kit and plugged the stock one back in and never had a problem since...
I replaced the relay on the fender but still does not prime the fuel rail all the time. I have to run a wire to the alt and the pump runs and primes the rail then starts , any ideas whats wrong thanks john